fix: overhaul the platform skeleton, add a serverless deployment track

An end-to-end audit found the repo could not build, test or run as shipped. This
fixes every finding, then adds a Cloud Run track so the demo costs about £1/month
idle instead of ~£150.

CI (red on its first run)
- api: setuptools could not build the package (flat layout with app/ and alembic/)
- web: missing @types/node; `vitest run` exited 1 with no test files
- pipeline: the stub run needed a gitignored VCF, and no process had a stub block
- ruff pinned, mypy configured, DB tests on real Postgres (pgserver locally, service in CI)

ML serving (scores were meaningless)
- the registered model now carries its own feature engineering and returns predict_proba,
  so serving sends raw columns and cannot drift from training
- resolve by registry alias (stages are deprecated in MLflow 3) and record the real
  version; re-scoring upserts instead of failing on the unique constraint
- ClinVar labels parsed from VEP's lowercase terms

Pipeline
- exact ref/alt recovered from a CHROM_POS_REF_ALT VCF ID; loading is idempotent
- job status reaches running/failed/succeeded, so the UI stops polling dead jobs
- DATABASE_URL travels in the environment or a Nextflow secret, never on a command line
- VEP cache and plugins staged as inputs; the gcp profile runs tasks on Google Batch

Deployment
- the API serves /api (matching the ingress); the web app reads its API URL at runtime
- migrations run in an init container under a Postgres advisory lock
- terraform: custom VPC shared with Batch, private Cloud SQL, API enablement, Workload
  Identity bindings, Secret Manager, deletion protection
- serverless track, now the default: Cloud Run services scaling to zero, a Cloud Run job
  for the Nextflow driver, and Neon or Cloud SQL behind one DATABASE_URL secret. GKE and
  Argo remain, behind -var deploy_kubernetes=true. See docs/cloud.md.

Correctness and security
- 409 on duplicate sample names, 422 on bad paging, natural chromosome ordering, wider
  VEP text columns, enum dropped on downgrade, the sample's assembly actually used
- vcf_uri restricted to gs:// objects or files under the data root, blocking option injection
- CORS restricted to configured origins; `make down` no longer deletes volumes

Data
- docs/data.md records the peer-reviewed, openly licensed sources (GIAB HG002, ClinVar,
  gnomAD) with citations and an honest evaluation plan; `make data` fetches a chr22 slice

Verified: api 50 tests, ml 18, loader 16, web 12; ruff, mypy, svelte-check, terraform
validate and both kustomize overlays clean.

infra/terraform/variables.tf

@@ -1,9 +1,59 @@
-variable "project" { type = string }
+variable "project" {
+  description = "GCP project id"
+  type        = string
+}
+
 variable "region" {
-  type    = string
-  default = "europe-west2" # London: keeps public genomic test data and the Cambridge team in one jurisdiction
+  description = "GCP region for every regional resource"
+  type        = string
+  default     = "europe-west2" # London: keeps public genomic test data and the Cambridge team in one jurisdiction
 }
+
 variable "github_repo" {
-  type    = string
-  default = "lynchaos/rarelens"
+  description = "owner/name of the GitHub repo allowed to push images via Workload Identity Federation"
+  type        = string
+  default     = "lynchaos/rarelens"
+}
+
+variable "deletion_protection" {
+  description = "Protect the GKE cluster and Cloud SQL instance from `terraform destroy`; set false to tear the lab down"
+  type        = bool
+  default     = true
+}
+
+variable "deploy_kubernetes" {
+  description = "Create the GKE cluster (Argo/ArgoCD track). Off by default: it costs ~$150/month idle, while the serverless track costs ~£1 (docs/cloud.md)"
+  type        = bool
+  default     = false
+}
+
+variable "deploy_cloud_sql" {
+  description = "Create a Cloud SQL instance (~$10/month). Off by default: set database_url to a free scale-to-zero Postgres such as Neon"
+  type        = bool
+  default     = false
+}
+
+variable "database_url" {
+  description = "Postgres URL used when deploy_cloud_sql is false, e.g. postgresql+asyncpg://user:pass@host/db?sslmode=require"
+  type        = string
+  default     = ""
+  sensitive   = true
+}
+
+variable "image_tag" {
+  description = "Image tag deployed to Cloud Run; CI pushes the commit SHA"
+  type        = string
+  default     = "latest"
+}
+
+variable "model_uri" {
+  description = "Optional model artifact to score with, e.g. gs://<project>-rarelens-data/models/pathogenicity/1. Empty means use the MLflow registry"
+  type        = string
+  default     = ""
+}
+
+variable "max_instances" {
+  description = "Cloud Run instance ceiling per service: scale-to-zero bounds the floor, this bounds the bill"
+  type        = number
+  default     = 2
 }